Terrestrial Snake Environmental DNA Accumulation and Degradation Dynamics and its Environmental Application

Kucherenko, Alexander S.; Herman, John E.; Everham, Edwin M.; Urakawa, Hidetoshi

doi:10.1655/herpetologica-d-16-00088

Cited by 43 publications

(58 citation statements)

References 37 publications

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“…This yielded a 58% detection rate using a quantitative PCR (qPCR) Taqman assay [66]. Another study confirmed these results by sampling sites with radio telemetry and burrow camera tracking [72]. However, unlike previous studies, soil samples were taken instead of water samples.…”

Section: Reptile Ednamentioning

confidence: 61%

“…However, unlike previous studies, soil samples were taken instead of water samples. Soil samples (~0.5 g) were extracted with a modified phenolchloroform protocol and amplified with conventional PCR for P. bivittatus using a CytB primer [72]. Importantly, the study found eDNA degraded over time in soil, becoming undetectable four to seven days after snake presence [72].…”

Section: Reptile Ednamentioning

confidence: 94%

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A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

et al. 2019

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Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, and present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have shown mixed results in detecting the presence of these animals under field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored non-avian reptile eDNA quantification by sampling four lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months to detect differences in eDNA using a qPCR assay amplifying the COI gene of the mtDNA genome. Only one sample of the highest-density pond amplified eDNA for a positive detection. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present the “shedding hypothesis”—the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms—as a potential challenge for eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

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Section: Reptile Ednamentioning

confidence: 61%

Section: Reptile Ednamentioning

confidence: 94%

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

et al. 2019

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“…Burmese Python ( Python bivvitatus ) eDNA began to degrade two days after snake removal and was 60% degraded after seven days [ 8 ]. Similarly, Red Cornsnake ( Pantherophis guttata ) eDNA has been shown to degrade in soil within a week [ 69 ]. This suggests that the temporal window for eDNA detection is brief and likely associated with recent snake activity.…”

Section: Discussionmentioning

confidence: 99%

“…In a massasauga population in Illinois, two of 100 crayfish burrows were positive for eDNA [ 13 ] while a study in Michigan found one positive detection out of 60 paired crayfish burrow water and sediment samples [ 54 ]. The one snake species where eDNA detection has had some success is the Burmese Python [ 8 , 67 , 69 ], a species that is significantly larger in size than C. kirtlandii or S. catenatus, suggesting that eDNA detection may be a function of body size within snakes [ 71 ]. More broadly, the greater amount and frequency of shed skin, mucus, and waste from amphibians and fish are hypothesized to make their detection much more tractable relative to snakes and turtles in freshwater systems [ 22 ].…”

Section: Discussionmentioning

confidence: 99%

Exploration of Environmental DNA (eDNA) to Detect Kirtland’s Snake (Clonophis kirtlandii)

Ratsch

Kingsbury

Jordan

2020

Animals

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Environmental DNA (eDNA) surveys utilize DNA shed by organisms into their environment in order to detect their presence. This technique has proven effective in many systems for detecting rare or cryptic species that require high survey effort. One potential candidate for eDNA surveying is Kirtland’s Snake (Clonophis kirtlandii), a small natricine endemic to the midwestern USA and threatened throughout its range. Due to its cryptic and fossorial lifestyle, it is also a notoriously difficult snake to survey, which has limited efforts to understand its ecology. Our goal was to utilize eDNA surveys for this species to increase detection probability and improve survey efficiency to assist future conservation efforts. We conducted coverboard surveys and habitat analyses to determine the spatial and temporal activity of snakes, and used this information to collect environmental samples in areas of high and low snake activity. In addition, we spiked artificial crayfish burrows with Kirtland’s Snake feces to assess the persistence of eDNA under semi-natural conditions. A quantitative PCR (qPCR) assay using a hydrolysis probe was developed to screen the environmental samples for Kirtland’s Snake eDNA that excluded closely related and co-occurring species. Our field surveys showed that snakes were found in the spring during the first of two seasons, and in areas with abundant grass, herbaceous vegetation, and shrubs. We found that eDNA declines within a week under field conditions in artificial crayfish burrows. In environmental samples of crayfish burrow water and sediment, soil, and open water, a single detection was found out of 380 samples. While there may be physicochemical and biological explanations for the low detection observed, characteristics of assay performance and sampling methodology may have also increased the potential for false negatives. We explored these outcomes in an effort to refine and advance the successful application of eDNA surveying in snakes and groundwater microhabitats.

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“…This may be best achieved by a combination of survey methods each targeting different groups of species (Garden, McAlpine, Possingham, & Jones, 2007). Potential alternative survey methods include time-constrained visual searches of quadrats (Barrows et al, 2016) pit-fall traps (Mengak & Guynn, 1987), and environmental DNA (Kucherenko, Herman, Everham, & Urakawa, 2018).…”

Section: Discussionmentioning

confidence: 99%

Hierarchical distance sampling to estimate population sizes of common lizards across a desert ecoregion

Furnas

Newton

Capehart

et al. 2019

Ecology and Evolution

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Multispecies wildlife monitoring across large geographical regions is important for effective conservation planning in response to expected impacts from climate change and land use. Unlike many species of birds, mammals, and amphibians which can be efficiently sampled using automated sensors including cameras and sound recorders, reptiles are often much more challenging to detect, in part because of their typically cryptic behavior and generally small body sizes. Although many lizard species are more active during the day which makes them easier to detect using visual encounter surveys, they may be unavailable for sampling during certain periods of the day or year due to their sensitivity to temperature. In recognition of these sampling challenges, we demonstrate application of a recent innovation in distance sampling that adjusts for temporary emigration between repeat survey visits. We used transect surveys to survey lizards at 229 sites throughout the Mojave Desert in California, USA, 2016. We estimated a total population size of 82 million (90% CI: 65–99 million) for the three most common species of lizards across this 66,830 km2 ecoregion. We mapped how density at the 1‐km2 scale was predicted to vary with vegetation cover and human development. We validated these results against independent surveys from the southern portion of our study area. Our methods and results demonstrate how multispecies monitoring programs spanning arid ecoregions can better incorporate information about reptiles.

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Terrestrial Snake Environmental DNA Accumulation and Degradation Dynamics and its Environmental Application

Cited by 43 publications

References 37 publications

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (Chrysemys picta) eDNA Under Field Conditions

Exploration of Environmental DNA (eDNA) to Detect Kirtland’s Snake (Clonophis kirtlandii)

Hierarchical distance sampling to estimate population sizes of common lizards across a desert ecoregion

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